Conserved design - the saving grace to understand life...

The internal design of living systems are similar despite the enormous external diversity. This fact of nature is quite handy to understand biology. Design of basic processes that propel life is conserved in organisms as diverse as microbes and humans.

For example, lets examine the common design in nature for energy harnessing,storage, and consumption - the key processes that make life possible. The energy source for all life on earth is the Sun (with the exception of life in deep sea vents [1]). Plants and certain bacteria have molecular machinery for harnessing energy from the Sun and store it in "battery molecules"[2].

The energy stored in these "battery molecules" is the source of energy for all life including plants that harness this energy. Living systems transfer the energy stored in these "battery molecules" into an "energy dispenser molecule"[3] that is used to perform any action, be it a human on a bike ride, or a bacterium rotating its tail[4] in a helical motion to propel itself. Life as we know it wouldn't exist had it not been for the capability of plants and bacteria to harness Sun's energy and store it in "battery molecules".

The energy stored in battery molecules (electrical energy standpoint) could be considered, from a mechanical energy standpoint, equivalent to picking up a boulder and placing it up on a hill. Plants did the work of pushing the boulder uphill using energy from the Sun. Now if the boulder is nudged to roll down, it comes accelerating down releasing all the stored energy. Its motion down the hill could be harnessed to do work (say toppling bowling pins!). However, if it was just a steep drop, the harnessing of energy from the fall may not be efficient since a good portion of it is lost as heat. Instead imagine the boulder rolls down a stairway where bowling pins are placed on each step. We could get a lot of bowling pins toppled while keeping the heat loss on impact minimal by breaking the fall into small steps. This is exactly what happens in our bodies. The energy from these battery molecules is extracted in intermediate stairway step like stages[5] during the fall down the energy hill, with the last stage extracting the maximum amount of energy[6].

Every time you flex your eyeball muscles as you read this sentence, you are extracting energy from battery molecules and transferring them to dispenser molecules that provide the energy needed to move your eyeball back and forth to read each line (you are also using vast amounts energy dispenser molecules to comprehend what you read). This is exactly the same energy extraction and dispensing mechanism the bacteria living in your mouth or your gut uses. Bacteria and humans share the same stages of energy extraction from "battery molecules". They have the same energy dispenser molecule; the molecular turbine in the last phase of energy extraction from battery molecules is essentially the same in both bacteria and humans ( this exquisite molecular turbine deserves a separate post).

There are indeed variations in the energy extraction machinery but the essential components are the same across living systems. We will examine more instances of core internal designs of nature being highly conserved[7].

Glossary and References

1. Deep sea ecosystems- Here sunlight is not the energy source since it is virtually absent in such depths. Instead of sunlight as is the case in terrestrial plants(photosynthesis), inorganic molecules or methane serve as the energy source(chemosynthesis). However even in these ecosystems the basic mechanisms of energy storage and dispensing are identical to that of terrestrial life.

2. Battery molecules - Glucose, glycogen are examples of battery molecules. Proteins and fats also serve as battery molecules providing fuel for cellular respiration(the process of converting stored energy in molecules to usable energy).

3. Energy dispenser - ATP is the energy dispenser molecule of living systems. With the exception of virus that relies on external energy sources, all living systems internally transfer the energy from battery molecules(e.g. glucose) into ATP to perform life functions.Once ATP dispenses the stored energy it becomes ADP which is recycled to produce ATP again by extracting energy from battery molecules (e.g. glucose).

4. Flagellum. The flagellum is a tail like structure that projects from certain cells and used for locomotion. In bacterium it is powered by a tiny motor that propels it forward. It is the same tail structure found in sperm cells to propel them forward. Wiki article on flagellum.

5. Energy extraction stages from battery molecules(e.g. glucose) - There are three distinct stages of extraction from a molecule of glucose. The first stage (glycolsis) yields two ATP molecules. The second stage (Krebs cycle) yields 2 ATP molecules. The last stage (Electron Transport Chain) yields 32 ATP molecules.

6. The last stage of energy extraction (Electron Transport Chain) is worth noting for the presence of a molecular turbine (ATP synthase) that rotates as it lets molecules fall down a concentration gradient (like the boulder fall downhill) and use the extracted energy to create the "energy dispenser" molecule. A 2002 article in Nature talks about scientists redesigning this molecule to make the first smallest switchable motor measuring 14 millionths of a millimeter across.

7. Biology - a Guide to the natural world - David Krogh - an excellent book to understand biology. Well written - thoroughly enjoyable.

Illustrative images/videos

Electron transport chain video - this shows the various molecular machines involved in creation of the concentration gradient needed to harvest 32 ATP molecules in the ETC stage.

ATP Synthase video - this shows the ATP synthase turbine molecule that is involved in the actual harvesting of 32 ATP molecules.

Muscle contraction video - 1

Muscle contraction video - 2. - these videos illustrate the role of ATP in muscle contraction.

Dimension in the microscopic world - Image - this image gives a sense of scale of the microscopic world of atoms, molecules, and cells.

Video synopsis of this post

Also on youtube

Biology - Discovering order in immense diversity...

When I recently read a Math teacher's lament (Paul Lockhart) on the plight of math instruction, I couldn't help wonder if there was an equivalent lament on the state of teaching Biology. I haven't found one yet. I share a similar sentiment for Biology instruction as Paul. His lament resonated so much with my own thoughts on the common misconceptions of what Biology is, particularly among those educated in India, where I did my schooling.

Biology is considered, in my circle of friends, synonymous with identifying the parts of an animal or plant! They cant be blamed for this misconception. Considering the diversity of life forms on earth, intelligent students realize early in their Biology curriculum, the futility of accumulating "store once, never recalled again memory", when they have to delve deep into the anatomy of select few species - cockroach, frog, plant... I don't recall learning any rationale as to why the deep study of anatomy of these few isolated samples of species would give me a panoramic view of living systems, their function, and their design. All I remember from those years of mindless cramming is a scattered vocabulary of terms - cloaca, ommatidia, parenchymatous cells etc. So most students quickly loose interest in it. Biology is shelved away in their brains as a boring discipline engaged in the pointless pursuit of identifying and naming the parts of critters and the likes.

Teaching Biology is perhaps even more challenging than teaching Math. Math is a product of abstract thought and is pure and beautiful at its core. It is liberated from reality - there are no imperfections, and rarely exceptions. Biology however, is more like engineering than mathematics. In fact it is "messy imperfect engineering" because there is no preconceived design. Living systems are the product of nature tinkering blindly over time. Imperfections abound in design. But it works. And those designs that don't work become extinct. To comprehend the underlying beauty of the design and order in living systems, one has to see through immense diversity and detail and identify common patterns of function and form that propel life in all its richness. That is hard. It is not like starting off with a few axioms and in short order experiencing the pleasure of proving an eternal mathematical truth. Having said that, perhaps Biology instruction can take that tip from Mathematics instruction - to start with as small a knowledge base as possible and focus on elucidating the underlying patterns and mechanisms of form and function rather than inundating our young with mind numbing diversity and detail. Being an engineer, I would have enjoyed and appreciated Biology if it was taught more like an engineering science where solving engineering problems are the path to learning and comprehension, as opposed to passive consumption of tons of detail (similar to Paul's statement of millions of adults remembering the formula for the solution to a quadratic equation, without knowing how it came about).

It gives me great pleasure to share the excitement and thrill of learning Biology in this blog for those, like me, who missed out on the fun of learning Biology(as it should be!) in their early life, and desire to have a glimpse of the beauty and order that propels life. I will continue to do this as I play catchup learning this thrilling, science of life.

One interesting side effect of my pursuit of learning Biology is that it is no longer possible to do some "unconscious actions" that I could do so easily before - I have to expend conscious thought and effort. For instance, I can no longer callously brush away that little pesky spider weaving webs in those hard to reach corners, or ignore that little ant and let it flush down the drain as it desperately clings to life on the edge with one leg stuck in a tiny blob of water. I am compelled to take the spider and leave it in the garden and engage in the "not so fast rescue operation" of that little ant (you cant scoop it with your fingers - it may become paste in the friction between your fingers and the surface you are scooping it from). And this behavioral change in me is not triggered by a new Buddistic view of life that captured my fancy, but from the simple realization that, that little ant or spider is much more complex and has millions of years of design that has gone into its making, despite it being "trial and error blind engineering", than the iphone in my pocket - a device that I so admire for its design, function, and beauty. And of course, a simple "drop test" comparison between my iphone and an ant proves the point - the resilience millions of years of what even blind design can produce. I am ignoring other minor comparison points such as self-replication...